The Plotgardener App

Source: vignettes/guides/plotgardenerApp.Rmd

Now Available!

The Plotgardener macOS Desktop App makes it easier to create publication-quality genomic figures with plotgardener. The app provides a simple point-and-click interface for building multipanel visualizations without writing code, and uses a dynamic parser to stay synchronized with the underlying R package.

Publication-quality genomic figures. No code required.

What is the Plotgardener App?

plotgardener is an R/Bioconductor package for building flexible, multi-panel, publication-quality genomic visualizations. It has been downloaded over a thousand times and cited in over 100 papers, but using it requires proficiency in R, package management, and the command line. For many biologists, that can be a significant barrier.

The Plotgardener App is a macOS desktop application that wraps the plotgardener R package in a graphical interface, making its full feature set available in a no-code environment. Users can add and configure Hi-C contact maps, signal tracks, gene models, genome labels, and more, all through point-and-click menus. Users can preview a live rendering of their figure as they work, and when the figure is ready, the app displays the underlying R script so that advanced users can copy and extend it further in any IDE.

Installation

The Plotgardener App is distributed as a single .dmg file that bundles all prerequisites in one desktop application for simple installation and usage. To get started:

  1. Download the latest .dmg here
  2. Open the .dmg file and move the application into the Applications folder
  3. Open the app and start building

The source code is open and available at: github.com/rishabhsvemuri/ThePlotgardenerApp

How it works

The interface is organized into four tabs:

Page: Set page dimensions and units before adding any plots.

Plots: Add, name, and configure as many plot panels as needed, chosen from a dropdown of all supported plotgardener functions. Each panel includes data upload via browse buttons, text parameter fields, and automatic validation of required inputs. Annotations can be layered on top of any plot panel.

Save: Save and reload your entire session as a structured JSON file, enabling figure templates and easy sharing between collaborators across machines.

Code: View the R script the app generates in real time. Copy it directly into an IDE for further customization.

Clicking Run Script compiles all panel inputs, executes the R script in a background session, and displays the rendered figure in the always-open preview pane.

Under the hood

The Plotgardener App is built on Electron and comprises three layers:

  • Frontend (React): Renders all user-facing tabs and form elements, dynamically populated based on the selected plotgardener function.

  • Backend (Node.js): Manages all parameter inputs, maintains panel state across additions and edits, compiles the final R script, and returns the PDF output to the preview pane.

  • Parser (Python): Parses the live plotgardener R package source (functions, parameters, and documentation) into structured JSON. This means the interface stays automatically synchronized with any updates to the package, with no manual maintenance required.

Source code & documentation